omnibioai-test-data/validate_test_data.sh at main · OmniBioAI/omnibioai-test-data · GitHub

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#!/bin/bash
# Validates test_data infrastructure completeness
TEST_DATA_ROOT="$(cd "$(dirname "$0")" && pwd)"
PASS=0
FAIL=0

check() {
  local desc="$1" path="$2" min_size_mb="${3:-0}"
  if [ -e "$TEST_DATA_ROOT/$path" ]; then
    actual_mb=$(du -sm "$TEST_DATA_ROOT/$path" 2>/dev/null | cut -f1)
    if [ "$actual_mb" -ge "$min_size_mb" ]; then
      printf "  OK    %-50s (%s MB)\n" "$desc" "$actual_mb"
      ((PASS++))
    else
      printf "  WARN  %-50s (only %s MB, expected >=%s)\n" "$desc" "$actual_mb" "$min_size_mb"
      ((FAIL++))
    fi
  else
    printf "  MISS  %-50s (not found)\n" "$desc"
    ((FAIL++))
  fi
}

echo "=== Reference Data ==="
check "hg38 chr21+22 FASTA"          "reference/human/hg38/chr21_22.fa"              90
check "hg38 chr21+22 FASTA index"    "reference/human/hg38/chr21_22.fa.fai"           1
check "hg38 full genome"             "reference/human/hg38/hg38.fa.gz"              900
check "mm10 reference"               "reference/mouse/mm10/mm10.fa.gz"              800
check "Gencode v44 GTF"              "reference/annotation/gencode.v44.annotation.gtf.gz" 40
check "STAR index hg38 chr21+22"     "reference/indices/star/hg38_chr21_22"         700
check "BWA index hg38 chr21+22"      "reference/indices/bwa/hg38_chr21_22"          250
check "Bismark index hg38 chr21+22"  "reference/indices/bismark/hg38_chr21_22"       90
check "CellRanger GRCh38 2020-A"     "reference/indices/cellranger"                 1000
check "Kraken2 standard 8GB DB"      "reference/databases/kraken2"                  7000
check "SILVA 16S sequences"          "reference/databases/silva/silva-138-99-seqs.qza"  90
check "dbSNP VCF"                    "reference/databases/00-All.vcf.gz"           15000

echo ""
echo "=== Test Data ==="
check "RNA-seq subsampled R1"        "test_data/rnaseq/test_R1.fastq"              100
check "RNA-seq subsampled R2"        "test_data/rnaseq/test_R2.fastq"               30
check "WGS NA12878 R1"               "test_data/wgs/NA12878_R1.fastq"              400
check "WGS NA12878 R2"               "test_data/wgs/NA12878_R2.fastq"              400
check "WES NA12878 R1"               "test_data/wes/NA12878_R1.fastq"              400
check "scRNA-seq PBMC 1k FASTQs"     "test_data/singlecell/pbmc_1k/pbmc_1k_v3_fastqs" 5000
check "ATAC-seq SRR5799393 R1"       "test_data/atacseq/SRR5799393_1.fastq"       1100
check "ChIP-seq SRR227563"           "test_data/chipseq/SRR227563.fastq"           1900
check "Methylation R1"               "test_data/methylation/SRR3368180_1.fastq"     50
check "Spatial Xenium outs"          "test_data/spatial/xenium/outs"               1000
check "Spatial Visium FASTQs"        "test_data/spatial/visium_brain"                1
check "Longread Nanopore"            "test_data/longread/nanopore_reads.fastq.gz"   20
check "Microbiome 16S"               "test_data/microbiome"                          7
check "CRISPR demo"                  "test_data/crispr/demo_library.txt"             1
check "Proteomics mzXML"             "test_data/proteomics"                        200
check "ctDNA analysis FASTQs"        "test_data/ctdna_analysis"                    800
check "SV calling FASTQs"            "test_data/sv"                                800
check "Epigenomics ChIP FASTQs"      "test_data/epigenomics"                         4
check "Multimodal CITE-seq"          "test_data/multimodal"                          6
check "Clinical variants TSV"        "test_data/clinical/sample_variants.tsv"        1
check "Drug discovery CSV"           "test_data/drug_discovery/compounds.csv"         1
check "Foundation model FASTA"       "test_data/foundation_model/sequences.fasta"     1
check "Metagenomics reads"           "test_data/metagenomics"                         3
check "Multiomics FASTQ"             "test_data/multiomics"                           4

echo ""
echo "=== SUMMARY ==="
echo "  PASS: $PASS"
echo "  FAIL/MISSING: $FAIL"
echo "  Total size: $(du -sh $TEST_DATA_ROOT | cut -f1)"